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This page was generated on 2024-03-27 11:38:00 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1703/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recoup 1.30.0  (landing page)
Panagiotis Moulos
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/recoup
git_branch: RELEASE_3_18
git_last_commit: 0d1e96b
git_last_commit_date: 2023-10-24 10:48:52 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for recoup on merida1


To the developers/maintainers of the recoup package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recoup.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: recoup
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recoup_1.30.0.tar.gz
StartedAt: 2024-03-26 07:21:57 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 07:35:33 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 815.8 seconds
RetCode: 0
Status:   OK  
CheckDir: recoup.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings recoup_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/recoup.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recoup/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘recoup’ version ‘1.30.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘recoup’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘GenomicFeatures:::GFF_FEATURE_TYPES’ ‘biomaRt:::.generateFilterXML’
  ‘biomaRt:::.setResultColNames’ ‘biomaRt:::martCheck’
  ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘biomaRt:::martVSchema’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘makeHorizontalAnnotation’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
readBamIntervals: no visible binding for global variable ‘bam.file’
recoupCorrelation: no visible binding for global variable ‘Index’
recoupCorrelation: no visible binding for global variable ‘Coverage’
recoupCorrelation: no visible binding for global variable ‘Condition’
recoupCorrelation: no visible binding for global variable ‘Design’
recoupHeatmap : <anonymous>: no visible global function definition for
  ‘grid.text’
recoupProfile: no visible binding for global variable ‘Signal’
recoupProfile: no visible binding for global variable ‘Condition’
recoupProfile: no visible binding for global variable ‘Design’
Undefined global functions or variables:
  Condition Coverage Design Index Signal bam.file grid.text
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
mergeRuns             43.884 10.274  43.077
profileMatrix         24.378 10.806  23.168
recoupPlot            17.537  5.165  16.721
recoup                17.486  5.121  14.107
sliceObj              16.276  4.749  15.314
kmeansDesign          16.706  3.996  15.029
simpleGetSet          16.084  4.461  14.780
recoupProfile          9.977  1.488  11.398
recoupHeatmap          9.477  1.404  11.510
recoupCorrelation      9.400  1.339  10.528
coverageRef            7.859  0.117   8.555
buildCustomAnnotation  5.169  0.264   5.771
calcCoverage           4.907  0.080   5.328
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/recoup.Rcheck/00check.log’
for details.



Installation output

recoup.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL recoup
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘recoup’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (recoup)

Tests output

recoup.Rcheck/tests/runTests.Rout


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("recoup")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'grid'

The following object is masked from 'package:Biostrings':

    pattern

========================================
ComplexHeatmap version 2.18.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite either one:
- Gu, Z. Complex Heatmap Visualization. iMeta 2022.
- Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
    genomic data. Bioinformatics 2016.


The new InteractiveComplexHeatmap package can directly export static 
complex heatmaps into an interactive Shiny app with zero effort. Have a try!

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

Getting main ranges for measurements
  measurement type: chipseq
  genomic region type: tss
Calculating requested regions coverage for WT H4K20me1
  calculating total coverage
  processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
  calculating total coverage
  processing chr12
Calculating profile for WT H4K20me1
Calculating profile for Set8KO H4K20me1
Constructing genomic coverage profile curve(s)
The resolution of the requested profiles will be lowered to avoid
increased computation time and/or storage space for heatmap profiles...
Calculating tss profile for WT H4K20me1
Calculating tss profile for Set8KO H4K20me1
Constructing genomic coverage heatmap(s)
Constructing coverage correlation profile curve(s)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
Getting main ranges for measurements
  measurement type: chipseq
  genomic region type: genebody
Calculating requested regions coverage for WT H4K20me1
  calculating total coverage
  processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
  calculating total coverage
  processing chr12
Calculating profile for WT H4K20me1
 center
 upstream
 downstream
Calculating profile for Set8KO H4K20me1
 center
 upstream
 downstream
Constructing genomic coverage profile curve(s)
Using provided design to facet the coverage profiles
Constructing genomic coverage heatmap(s)
Using provided design to facet the coverage profiles
Constructing coverage correlation profile curve(s)
Using provided design to facet the coverage profiles
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")


RUNIT TEST PROTOCOL -- Tue Mar 26 07:35:16 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
recoup RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 78.099  16.946  78.045 

Example timings

recoup.Rcheck/recoup-Ex.timings

nameusersystemelapsed
buildAnnotationDatabase0.0000.0010.001
buildAnnotationStore0.0000.0000.001
buildCustomAnnotation5.1690.2645.771
calcCoverage4.9070.0805.328
coverageRef7.8590.1178.555
coverageRnaRef0.0010.0000.001
getAnnotation1.4220.0573.793
getBiotypes0.0010.0010.001
getInstalledAnnotations0.0020.0020.003
importCustomAnnotation1.7700.0231.832
kmeansDesign16.706 3.99615.029
loadAnnotation0.0020.0010.003
mergeRuns43.88410.27443.077
preprocessRanges0.3970.0370.454
profileMatrix24.37810.80623.168
recoup17.486 5.12114.107
recoupCorrelation 9.400 1.33910.528
recoupHeatmap 9.477 1.40411.510
recoupPlot17.537 5.16516.721
recoupProfile 9.977 1.48811.398
removeData0.0210.0100.030
rpMatrix1.4200.2151.850
simpleGetSet16.084 4.46114.780
sliceObj16.276 4.74915.314